Contacts of the strand formed by residues 395 - 399 (chain P) in PDB entry 1VYH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 395 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P ILE 5.6 1.3 - - - +
96P PRO* 5.0 13.0 - - + +
116P PHE* 4.4 0.2 - - - -
354P LEU* 5.7 4.3 - - + -
362P LEU* 4.8 13.0 - - + -
386P LEU* 4.8 9.9 - - + -
387P ASP 3.6 17.5 - - - +
388P PHE* 3.3 37.2 - - + +
393P PRO 5.3 0.9 - - - +
394P TYR* 1.3 80.3 - - - +
396P VAL* 1.3 73.7 + - - +
397P THR* 4.5 6.5 - - - +
406P VAL* 3.5 1.6 - - - -
407P TRP* 2.7 48.3 + - + +
408P GLU 5.6 0.6 + - - +
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Residues in contact with VAL 396 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P VAL* 3.6 16.6 - - + -
116P PHE* 3.0 38.6 - - + -
123P MET* 3.9 20.9 - - + -
137P TYR* 5.0 1.6 - - + -
386P LEU* 3.4 1.2 - - - -
387P ASP 3.0 29.7 + - - +
395P VAL* 1.3 76.0 - - - +
397P THR* 1.3 68.7 + - - +
404P VAL* 3.5 26.0 - - + -
405P LYS 3.0 18.2 - - - +
406P VAL* 4.1 12.3 - - + -
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Residues in contact with THR 397 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114P VAL* 4.0 5.4 - - - -
356P CYS* 6.0 0.2 - - - +
362P LEU* 4.4 13.3 - - + +
378P ALA* 4.6 4.9 - - + -
379P HIS* 2.8 38.5 + - + +
383P VAL* 3.6 19.1 - - + -
385P SER 3.5 5.2 - - - +
386P LEU* 4.1 10.4 - - - +
395P VAL* 4.5 1.4 - - - +
396P VAL* 1.3 77.5 + - - +
398P GLY* 1.3 60.2 + - - +
404P VAL* 3.1 6.9 - - - +
405P LYS* 2.7 32.9 + - - -
407P TRP* 3.5 24.9 + - - +
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Residues in contact with GLY 398 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P VAL* 4.6 6.7 - - - -
114P VAL* 3.7 16.8 - - - +
379P HIS* 4.1 2.7 - - - -
383P VAL* 3.4 3.6 - - - +
384P THR* 2.7 29.0 + - - -
385P SER* 2.9 21.4 + - - +
397P THR* 1.3 75.9 - - - +
399P SER* 1.3 55.0 + - - -
403P THR 3.7 8.5 - - - -
404P VAL* 4.5 0.9 - - - -
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Residues in contact with SER 399 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P VAL* 2.9 27.8 + - - +
379P HIS* 3.0 19.7 + - - +
381P HIS 3.7 1.3 + - - -
382P PHE 2.9 24.2 - - - -
383P VAL* 3.3 12.1 - - - -
384P THR* 3.7 7.4 - - - +
398P GLY* 1.3 73.9 - - - -
400P VAL* 1.3 67.7 + - - +
401P ASP* 2.3 34.8 + - - -
402P GLN* 3.8 4.0 + - - -
403P THR 3.5 7.1 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il